Analysis of AAV vector integration in in vitro and in vivo reprogramming into pluripotency

In this study we have reprogrammed mouse somatic cells into induced pluripotent stem cells (iPSC) in vitro and in vivo using adeno-associated viral (AAV) vectors expressing Oct-3/4, Klf4, Sox2 and c-myc. After observing AAV vector traces in all our AAV-derived iPSCs, we performed non-restrictive linear amplification-mediated PCR and target enrichment sequencing to analyze the potential AAV vector integration events. We determined that most of our AAV-derived iPSC had AAV vector integrations, which were located mainly in introns and in intergenic regions. We hypothesize that these integrations occur likely due the increased genome accessibility during the reprogramming process. To our knowledge, this is the first time that AAV vector integration during reprogramming is thoroughly characterized, so this study can help shedding some light into the mechanisms and consequences of AAV vector persistence.